As populations diverge, their genomes acquire changes that render them incompatible, generating reproductive isolation between the populations. This process provides a unique window into how naturally occurring genetic variation can generate effects that, when combined, produce deleterious consequences for an organism's survival or fertility. To investigate how these effects arise and what their consequences may be, I plan to combine bioinformatics and experimental approaches, utilizing incipient and recently formed species throughout the Drosophila nasuta complex as a study system. Specifically, I will first characterize divergence between pairs of genomes throughout the complex on both global and local scales, in order to identify candidate regions of exceptionally high divergence and to assess how genomic characteristics such as structural variation may play a role in generating or reinforcing such regions. Second, I will use statistical analysis of population data derived from experimentally maintaining hybrids between inter-fertile species over many generations to infer the location of deleterious epistatic interactions contributing to reproductive isolation. Third, I will use a combination of bioinformatics analyses, behavioral assays, and experimental genetic approaches to identify the mechanisms by which the identified genetic regions contribute to reproductive isolation. The results of this study will inform our understanding of the ways in which changes throughout the genome contribute to such deleterious phenotypes as infertility, and will enhance our knowledge of the inter- connectedness of the genome.